Metroid FISSION
by Tyrammafar
Summary: A week after the 'X incident', Samus finds herself caught in a war spanning hundreds of years and a thousand worlds. Now that she is involved she must choose a side, and what path she chooses will change the galaxy and the way she sees life...forever...
1. The Mission Gone Wrong

**A Metroid/original story crossover. The story that is crossed over is one written by me, and though I do not own the character Samus Aran, Metroid, the X, or any of those things, the world this takes place in, and all other characters, belong to me. This story is researched, as far as scientific things go, and takes place one week after the incident with the X Parasites and SA-X. **

**My first Metroid fiction, though not my first use of Samus Aran herself. It begins in first-person, than goes to third.**

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**Metroid Fusion:**

**FISSION**

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**Chapter 1**

**The Mission Gone Wrong**

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_It has been a long, long time since I first went back to Zebes…to destroy Mother Brain. It has been so long since I hated the Metroids, but now they are not only my friends and allies, they are my cousins as well, genetically speaking. I hate to think of them as energy-sucking bastards now, since I know more about them than any human ever could. Because now I am no longer human._

_The computer…Adam…is still around, still hassling me about things I do wrong, and the things I do right are no cause for praise. Just like he was before his mind was transplanted into this ship. I never thought I'd say it, but I'm glad _someone _remotely human, if long dead, is out here in space with me._

_Much better than the one sitting in the co-pilot's seat next to me…wearing a hideously blackened mockery of my power-suit. So vile, twisted…it should never have come into existence…and yet, I love it like a son or daughter. Nothing would ever change that, and it is all thanks to that incident two years ago…with the X parasites. Those things made me into what I am, a half-human/half-Metroid freak of nature. No…not of nature; of science. _

_I sit here in this chair, breathing in the thin air of the ship that has been my home for a month now, and think back to when my 'partner' and I first met. Or rather, when it held a gun to my face and hissed in some vile language that I didn't understand at the time. Terrible way to make a first impression, but it wasn't old enough to understand that at the time. _

_I think back to when I first met this wicked horror, this unholy _fusion _of two evils. This is what my life is now, and though it does little good to dwell on the past, it helps me think more about the future. If I live long enough to see it, that is._

_It all began many months ago, on an asteroid far out in space…a little salvaging on my part. I never realized that in a few short days time my world would be torn into bits, melted, blasted with cryogen, and then put back together inside-out. Yeah…that's about how bad it was, but I couldn't see it coming until it hit me full in the chest like some mutant, demon grizzly bear…_

_-Samus Aran_

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_**Many months earlier…**_

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Samus Aran sweated inside the power-suit, tired after climbing over jagged rock and leaping over chasms for three days straight. She didn't have to sleep as often, but she slept longer, thanks to the Metroid DNA in her system. She sighed, looking out over yet more bleak, unforgiving asteroid landscape, a beep in her helmet bringing her to attention.

"What is it, Adam?"

"_Come on, Lady, what are you doing out there?"_ The computer said. _"Why haven't you found that old ship yet?"_

"It isn't here! Whatever energy source you detected is either gone or it never existed." Samus crossed her arms, the cannon on her right collapsing into the smaller blaster instead of the spazer. "You must have messed up your scans…"

"_I know it's there…you must be right on top of it! You are within twenty feet now, can't you look around?"_

"Wait…say that again?"

"_I know it's there…you must be right on top of it! You are-"_

"Stop!" Samus shouted. "You said…right on _top _of it! Could it be underground?"

"…_there is a distinct possibility."_ The other admitted.

"Well, I'm going to blow this little area up, and see what's twenty feet below me. Two megaton or three?"

"_Are you…are you going to use a power bomb?!"_

"Why not?"

"_You really are insane, Samus!"_ The computer cried. _"Don't you dare! You could make this asteroid incredibly unstable."_ Samus scratched her stomach, though the suit prevented her from getting to the itch.

"Yawn." Samus didn't actually yawn, she just said the word. "Any other options…_besides _digging?"

"…_tunneling?"_

"Are you that determined to get me to do this?" Samus asked, impatient after so long without a break. "What's so important about this ship anyway?"

"_It is old beyond belief…older than human technology, and even the Chozo technology on Zebes! This could be beyond the birth of life on Old Earth…"_

"And what does this do to help us?"

"…_there might be a reward."_

"I'm listening now." Samus tried to scratch the itch on her stomach again, but it only got worse and now she gave up, crouching and looking at the ground. "So, what will it take to get down to it?"

"_Not much, really. With your power-suit, it will take maybe an hour's digging time to reach it."_

"That's not so bad…" Samus paused, standing and looking down at her stomach, though her suit was in the way. "Adam…something might be wrong."

"_What is it, lady?"_

"I think something bit me…I have this bad itch on my stomach and it...it's burning now."

"_Do you require medical treatment?"_

"Let's play it safe…"

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Adam began to bring the thrusters online, powering up the ship's systems. He had never told Samus that he had been able to do this, and when she found out herself she never mentioned it. The computer began to lift the ship off of the asteroid plateau that it was on, tracking Samus's position nearly on the opposite side of the asteroid.

Then he heard it…a scream, coming in through the communication link to her power-suit.

"Samus!"

"_Oh God, damnit, it hurts!"_

"What is it, Samus?!" Adam put more speed into his ascent, becoming very worried…in a simulated sort of way. "Speak up, lady!"

"_My stomach! It hurts! Holy mother fu-"_ The comm. went dead.

"Samus?" Adam asked quietly. "Samus, what happened?! Samus! SAMUS!" He began throwing out a distress signal in all directions as he flew towards the human's position as fast as he possibly could without blasting the ship apart in the asteroid's thin atmosphere. "Don't worry, girl, I'm calling for help…"

And to his great surprise, and joy…someone answered.

Adam landed and opened the bottom hatch, hoping Samus would find a way inside…

…if she was still alive…


	2. The War

**I had to compress two chapters into one in order to speed this story along to the main plot, and so a lot of unneeded information in this chapter was removed to allow the two to be out together. This whole chapter is not very good in my opinion, but it will get this story onto its feet sooner, and get us to gripping the edges of our seats in no time.**

**Sorry for having to do this, but the next few chapters will explain what is going on more than this one does.**

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**Chapter 2**

**The War**

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_Hell, now that I _do _look back, my life didn't quite suck until that one moment when I felt like my stomach was being eaten by a satanic cockroach. Really, I was in pain; I haven't actually cried in my life that I can remember, but I did then. It was like being torn apart…_

_And then it only got worse. Maybe I should just not say a word, but then this tale would be over…I have to tell the story, or it might be lost forever. If not me, then maybe someone else can learn from my mistakes…_

_-Samus Aran_

_---------------------_

Samus opened her eyes to bright light above and all around her, and the steady beeping of machines. They were counting her pulse, she knew, it had to be that, and the sound increased its rate of beeping when she opened her eyes. She heard a few voices, and then saw a shadow over her face, and then heard a clearly human voice.

"She's awake! Bloody hell, I thought she was in a coma!" The man said, looking away from her face. The rest of the room was out of focus, but she appeared to be on a bed with several other beds lined up along the walls. She was not wearing her helmet, she realized, and her suit was gone. Without it, she felt totally naked…which she was. "Jeffries! Get the hell off the game and look at her already!" The man yelled as another man ran to her side. Samus pulled the white blanket closer to her as she sat up, blinking in the horribly bright light. It was cold, extremely cold…it was almost artic in her opinion.

"What the hell is the temperature in here?" Were her first words.

"Seventy-six degrees since the climate control systems went haywire in this sector." The man to her left said, this one younger and beardless. The other, the first to speak, had five-o'-clock shadow. "How are you doing?"

"I'm freezing my ass off." Samus snapped. "It feels like Deep Maridia all over again in here!"

"It may be because you might be sick." The older man said. "We only got you into this med lab a few minutes ago, and we haven't had the chance to scan you properly. What is your name, by the way?"

"Samus Aran." She answered instantly, blinking as the room came into focus. The walls were stark white, and so was everything else, like the room had been filled with bleach before it was used.

"Well, Samus, I'm Dr. Isen, and this is Dr. Jeffries, my assistant." The older man said from her right, handing her a hospital gown, which she was able to put on under the sheets.

"You haven't heard of me?" Samus asked, confused.

"Should we have?" Dr. Jeffries asked, raising an eyebrow.

"Nevermind…where's my suit? Where's my ship?"

"Your suit is in quarantine in that closet over there." Dr. Isen pointed to the far side of the room. "And your ship has been sitting on docking pad number three bugging our own AI for more than twenty minutes with random bits of code."

"I need my suit…" Samus said, sliding out of the bed and standing on the ice-cold floor.

"You shouldn't be up!" Dr. Jeffries cried, trying to pull her back down, but as he grasped her shoulders and shoved her back towards the bed, she didn't budge.

"I'm a lot stronger than I look." Samus said, straightening her blonde hair. "Now, I need my suit."

"I'm afraid we can't let you back into it until we've had you scanned." Dr. Isen said. "Please, sit down for a moment." Samus scowled and did so, missing the weight of her arm cannon. She hadn't taken that suit off in a week, ever since the X Incident, as she had come to call it. She noticed now that she had a long cut on her left forearm, and she instinctively looked around for a glowing yellow ball to absorb into herself…but remembered that the X were extinct now, and she couldn't heal herself that way anymore.

Dr. Jeffries was now at her side with a large handheld computer, which emitted a faint humming sound at all times. "Go ahead and lay down." Samus obliged, grimacing at the cold that seeped into her bones. A thin beam of red light ran from her feet to her head and back down to her feet, and then the computers around her hummed even more. "This could take a little while, just relax, Aran."

"Samus will do, I'm not a soldier."

"By the quality of that Bio-suit, I'd think you were."

"Bio-suit?" Samus asked.

"A suit made to act like living flesh, flexible and tough, and also able to heal itself over a period of time. When it's on you, anyway. But that one healed a cut on its forearm in a matter of an hour, from when it was cut to when you first got here." Dr. Isen explained. The little handheld beeped in Dr. Jeffries's hand.

"Dr. Isen, the scanner is going insane again." He said angrily.

"What is it showing now?"

"It says her DNA is only sixty-percent human, the rest is unidentified."

"No surprise." Samus muttered, smiling slightly.

"Pardon?" Dr. Jeffries set down the little device.

Samus cleared her throat. "To make a long story short, I nearly died and some Metroid DNA was added to my own and saved my life. That is probably why it's so cold to me in here; my body is now able to be frozen if it is colder than forty degrees Fahrenheit."

"One…that seems impossible." Dr. Isen said. "Two, I have no idea what a Metroid is…and three, why is five percent of that DNA from an X parasite?"

"Because I absorb them to heal my wounds and gather powers that they stole from me." Samus said, sliding out of bed again, despite the two men's protests. "Now, if you don't get me my suit, I will most likely die of hypothermia." They hesitated before leading her across the room, opening a sliding white door. The Fusion Suit was laying in pieces in a pile by the door, and Samus walked in, sealing the door behind her.

---

"Dr. Isen?"

"Yes?"

"She said she can absorb the X parasite?"

"She did."

"Does that mean…we've found a way to kill them?"

"I think we have."

---

Samus opened the door, the suit's systems powering up and her arm cannon charging up. "Alright, next on the list…why the hell did my stomach feel like it was ripped open?"

"Nothing appeared on the scanner that would cause such a thing." Dr. Isen said. Samus scowled inside her helmet as she saw a blue-uniformed man beside the doctor. "Samus Aran, this is Captain Francisco." The doctor said, and the man smiled and bowed his head a little. He was Spanish, that was plain, but he had something else in him that she couldn't identify.

"I've heard a little about you, Miss Aran."

"Samus."

"Samus…you are supposedly able to kill X parasites?"

"Yes, and?" Samus tapped her arm cannon, three locks disengaging and expanding the end of the barrel to switch it into spazer mode.

"I think we may have a job for you, Samus." The Captain said. Samus looked him right in the eye, drawing close to him so that he could see his reflection in her visor.

"There…are more?"

"A whole planet of them." The Captain said. "_Our _planet. This ship and a few others are all that is left."

"No."

"You are in no position to argue, Miss Aran…you are in our space, and under our jurisdiction." The Captain said calmly. "You are, unofficially, being drafted it seems." Samus raised her arm, the cannon charging, placing the heating barrel right on the man's chin.

"Draft this, fucker."

"I like your style, but that won't work." He said, but he was not feeling as calm as he was before, Samus could almost smell it…he was afraid of her. "Now I will offer two choices…either you help us find a way to kill off these X, and you go home, or we freeze you in a tube and blast you into space."

"Federation law doesn't allow-"

"This isn't any Federation, Miss Aran." The Captain interrupted, gripping the arm cannon and pushing it to the side. "This is a whole new ballpark…the Federation is about thirty parsecs away, and this is _our _space."

"…so I do or die? Is that it?"

"That is it."

"…I don't like either option, but I'd much rather wipe these X out than be frozen for several years." Samus let the energy she had charged into her cannon subside. "So they have taken over the _entire _planet?"

"All of it, above ground and below. Land and sea. Air and space. This is an X world right now, but we hope to change that." The Captain said. "What training have you received?"

"None."

"None?"

"Do extinct alien races count?"

"I'm afraid not." The Captain said. "How many years of experience, then?"

"Twenty." Samus said. "I've been blowing the brains out of aliens since I was four…and I don't plan to stop any time soon."

"She's as good as any." The Captain said. "Welcome to the little freedom force we have, Miss Aran."

"Samus." She corrected.

"You will have to start somewhere, Samus." He said. "When your ship sent out that distress call, we were planning on sending an advance team down to the planet's surface to try and find out if anyone in our fallout shelters survived. I want you to go with the squad."

"I work better alone."

"And my men work better with a badass mutant Cyborg with a gun for an arm by their side." The man retorted, nodding towards Dr. Isen. "Is she healthy?"

"Fitter than any human on board this vessel, sir." He said.

"Time to move on, Miss Aran-"

"Samus."

The captain ignored her. "-we have places to go, things to kill."

Samus followed the man to the far side of the room, where he pressed his palm to a door panel, the door sliding upwards into the ceiling. Like the medical lab, the hallway was undecorated and stark white, and Samus saw no one walking past. She followed the man to the right, past several closed doors, before taking another right though one, entering a room that was vastly different from the lab and hallway. This room was dark, hot, and humid, and to Samus it was almost perfect.

Except for the five men around the room, strapping on combat armor. They all snapped to attention when they saw the Captain. "As you were." The men went right back to what they were doing. "Change of plans, ladies, you have a new squad member, this Samus Aran. Nothing else has changed, you know your orders?"

"Yeah, Captain, we know 'em." A man with dreadlocks said, scratching his goatee. "How's are we goin' ta get _into _the sheltah is what I'm askin'."

"That's up to your Commander." The Captain nodded to a bald man in the corner, leaving the room.

_Damnit, I hate soldiers. _Samus thought. _First I get drafted, now I have to work with these idiots. _

There were five men, all of them with plates of green metal strapped to their bodies. Each one wore a hard expression, except for the one with dreadlocks, who was smiling about something she couldn't identify. The Commander was large, bald, and insanely muscular, as if he was training himself to crush boulders with his pinkies. Another was thin and pale, and had a blank expression and a slight twitch in his right hand. The next was short-haired and of average height and weight, but he carried a large minigun under his shoulder. The last was so dark-skinned that he melted into the shadows in the corner, his eyes watching her every movement.

And Samus hated every one of them. "So what exactly _are _you?" The Commander asked. "Are you a Cyborg?"

Samus ignored him.

"Well, I'm your new CO, I suppose." He said. "This man in the corner with the nasty look is Wraith." He pointed to the black man. "The one with the big-ass gun is BlackJack. The kid over there- wipe that smile off your face!- the kid is Spark, cause he keeps getting his taser out and zapping himself on low power…freak…and the guy with the nasty twitch is…well, Twitch."

Samus turned away, not answering.

"Alright, I can understand that, you don't want to talk."

"Leave it alone." BlackJack said, polishing the metal that made up the rotating barrels of his weapon. "Cyborgs never talk."

"He's not a Cyborg, you idiot. Cyborgs answer when they are spoken to." Twitch said, clenching his fists.

"Fuck you."

"Damnit, Jack, be quiet." Wraith said from his corner, blowing dust from a clip and sticking it into the bottom slot on his rifle.

"Fuck you, too!"

"Shut up!" Their Commander yelled, grabbing Jack by the back of his shirt. "Get yourself together, I know you have issues but keep them to yourself."

_Damnit, it just keeps getting better and better, doesn't it? _Samus thought, switching her arm cannon back into blaster mode. _And let me guess…it's only going to get worse, right? _Samus tapped the side of her helmet, activating the communications channel with Adam. "Adam…are you there?" She said, her external speakers off so that the others wouldn't hear her.

"_Samus?"_ The AI sounded…desperate, deathly afraid. _"Samus! Are you alright?! What happened?!"_

"I've been drafted, that's what happened."

"_What do you…drafted?"_ The computer paused. _"Samus, what's going on?"_

"The captain of this ship wants me to help eliminate the X parasites on the planet that we are supposed to be in orbit around…and I will help."

"_Samus, thought you already know it is, I have to tell you anyway. This is a suicide mission."_

"So is every one I've taken before."

"…_point."_ Adam gave a mechanical sigh. _"So what does this mean for me?"_

"You are going to take off and get into an orbit over where I am, and that way I can still get maps and scans from you."

"_You are planning some of this ahead this time, I see."_ Adam muttered. _"I will begin taking off now…are you going to be alright?"_

"I'm a tank on two legs…I'll be fine, Adam."

"_I truly hope so…" _The AI paused. _"What about the pain in your stomach?"_

"Gone, and the doctor scanned me as well. Nothing is wrong with me."

Adam was not convinced_. "Still…take care of yourself, and if you have any other signs that it might happen again, contact me that instant."_

"I hear you, I will make sure to. Good flying, Adam."

"_Don't die on me down there, lady…"_ The comm. went off as the ship went out of range.

"…I'll be the only one still alive down there come tomorrow, you can be sure of that…"

**There, a much abridged chapter to get this show on the road so we can watch some death and violence! **


	3. Planet X

**Freaky stuff right here…**

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**Chapter 3**

**Planet X**

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_Sometimes I think that the entire human race is completely insane. The humans that made up my squad were, and they knew they were for doing this shit. I knew they were crazy, they knew it, Adam knew it, the Captain knew…hell, I think even the damned X parasites knew it! Why was I going along with this crazy idea of theirs?_

_Because of the Metroids. I had nearly half the DNA structure of a Metroid, and with it came some of their behavior…I wanted to hunt down the X because they were my prey, and I also knew that if I wasn't there then the planet would have been lost, and the X would take over the universe. I couldn't let that happen, and the Metroid in me wouldn't let that happen. _

_I would smear those nasty little SOBs all over the damned ground, and then I would soak them up like a sponge and become even stronger. This is what I do now…it was what I did before…I'm a Hunter, and now the X are my prey._

_-Samus Aran_

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"We're coming into the atmosphere now!" The pilot of the dropship yelled, the lumbering craft coming close to the planet's surface. "Command doesn't want me to land, so we're going to have to just drop you on the floor!"

"Adam, come in."

"_I'm right here, lady._" The computer said in her ear. _"How is it going so far?"_

"Very well, actually." Samus adjusted the straps that were pressing against her suit, holding her into the little pod that was much like a cyrotube. "We're about to be dropped in onto the planet's surface…how's it look from up there?"

"_Bleak and depressing, but I'm a computer, so what do I know?"_

"I'm talking about the X…"

"_Oh…nothing so far, but I am picking up traces of X DNA all over the place, but no bio-signs. When you get on the surface, keep your weapon half-charged to let you fire faster."_

"I will." Samus heard a sharp clicking noise and her stomach lurched. "AHH!" The pod rattled and the air inside began to heat up, and Samus felt like she was being pulled though a pinhole by her nose. Her stomach felt for a second like it was going to rip apart again, but this went away after a moment. Samus thought it couldn't get any worse of a drop than this…and then she landed.

There was a deafening clang, the pod crunching and the metal shrieking. Samus hit her head on the panel in front of her, her vision going dark for a moment. There were a few clicks at the hatch released and a blast of air as it was jettisoned.

The hatch stayed where it was, keeping her locked in, and Samus kicked it out instead, hot air hitting her. The capsule was blackened from entry, and she looked around for the other pods, which she saw dropping a few hundred feet away behind some trees.

The planet was covered in forest, and thought it looked as though there would be insane amounts of life…there was none. No birds called, no animals cried out, and nothing moved the branches of trees or the grass below them. The area was completely and utterly lifeless, the sun hidden behind an overcast sky.

"We've landed." Samus said.

"_I saw…are you sure you didn't get whiplash from that impact?"_

"I'm fine, just a little shaken." Samus tapped her arm-cannon, making it hum slightly as it charged half-way. "I'm going to rendezvous with the rest of the squad, before they get infected by any X…wherever the X are." Samus began to move away from the pod slowly, eyeing the trees around her and listening for anything out-of-the-ordinary. There was a feeling in her chest that told her that she shouldn't be here, and yet it also made her _want _to be here. It was the hunter's instinct.

"Squad, report in!" The CO yelled over the communications link.

"This is Wraith, reporting in, all clear on the scope." A deep voice said.

"This is T-Twitch, ready for orders, s-sir!" A thin, hollow voice stuttered.

"BlackJack, reporting in all clear, nothing but silence all around…I want to break it, though." This one had a Texan accent.

"Dis is Spark, all ready ta go and get da little buggahs!" The last one said. There was a crackle over this man's channel. "Eh, I be bringin' the monitahs online, ya'll see anything?" Samus saw five little boxes appear in the top-right of her HUD, labeled with each man's name and vital signs. Twitch had double the heartrate as anyone else.

"I see it." The commander said, and Samus saw that a little speaker icon appeared next to the box labeled 'Corpse'. "Wait a second, Aran, report in!"

"This is Samus Aran." Samus said. "I have your lifesigns on my HUD."

"What the hell…you're a woman?!" Black Jack yelled over the radio as Samus moved towards where they were supposed to have landed.

"I guess so…we haven't heard you say a word until just now." Wraith muttered. "Hey, Twitch, look to your left!"

"AH! Oh…h-hey, W-Wraith! You…scared…me…"

"Damnit, everything scares you!" The other replied. "Get over here and let me see your radar!" Samus came to an area where the trees grew less dense, and there was grass growing on the ground below her boots. The sky was concealed behind gray clouds that looked as if they might shed rain at any moment, and the trees were very green. The grass was a little more blue than she was used to seeing, but otherwise this was much like the plains on southern Zebes.

"There's nothing that I can see, sir." BlackJack said.

"Nothing on Twitch's radar." Wraith said. "I think we're all alone…for now. We better find the shelter in this sector before the X get curious."

"I'm all for it." 'Corpse' said. "Alright, Samus, send a bolt up where we can see it, seeing as how you are the only one here with an energy weapon. We'll group where he…she…is."

"I hear you." Samus raised her arm, discharging a bolt of blue energy that sucked the heat out of the air around it. The bolt shot into the air, and then turned into a cloud of bluish vapor that sparked and glittered.

"Pretty…alright people, move towards it!"

Samus waited there, her arm-cannon recharging. Samus thought then, for the first time in a week, that she was now doing something for the sake of humanity, not just because se was ordered to. She wanted to get rid of the X for good, and this was as good a start as any. The thought of the X made her think of the late Ridley, her former nemesis and the one who had made her an orphan twice over. Even though she hated him…she wished that the pirate hadn't been killed by the X…no being alive deserved such a terrible fate. She would much rather fight Ridley than any X; at least he had been another living being, the X were just killers, plain and simple. Chances were that there were no humans left on this planet but the five soldiers and herself. No…not herself; she wasn't a human anymore and couldn't be counted. She turned to her left as three of the men came through the trees; Wraith, Twitch, and BlackJack.

"Samus, there you are." Wraith said, holding his high-powered rifle close to him, as if it might vanish suddenly. "Any sign of the X?"

"Nothing as far as I can see…and I've seen it all before." Samus muttered. "There's Corpse…and Spark." Sure enough, the two other humans were approaching from the right, Corpse in the lead with an assault rifle, and Spark behind with a long weapon that looked a lot like a cattle prod.

"All accounted for?" Corpse said.

"All accounted for." Wraith repeated, nodding. "The fallout shelter is to the north…we should head there as soon as possible, so the X don't catch our scent."

"They already have." Samus said in a low voice.

"How do you know?"

"One…I know the X better than any of you, I had to deal with them for four days straight inside a science station. Two…five percent of my DNA is from the X…if I can smell you, so can they." Corpse scowled and nodded to Twitch.

"Lead the way, you have our radar." The soldier nodded vigorously, shaking and turning around to almost walk-run towards the thicker trees. "Other way, Twitch…"

"Oh! I-I knew that! Just got t-turned around…that's a-all!"

--------------------

The squad fell in step behind Twitch, who was carrying a screen in his left hand and a sub-machine gun in his right, which had the safety on because he had a twitchy trigger finger. The screen was blue, and showed everyone there in red, as well as anything else that might be alive around it.

Behind him was Corpse, rifle at his shoulder and eyes squinting into the shadows around them, searching for any sign of life, human or otherwise. Then there was Wraith, who remained silent, and then Spark, still smiling, and finally BlackJack, who kept glancing behind at Samus in the rear. The forest didn't change much, and though to most it would look all the same, Samus had learned to pick out things around her to find her way when she was first on Zebes, and she knew that they were still heading north.

"We are getting close to the bunker." Wraith said, pointing ahead to the thickening trees. "They are built mostly underground, and whenever anything happens the civilians flock to them. I just hope the X didn't get into them…"

Samus didn't answer, she didn't need to. She switched her visor to combat mode, several blips appearing ahead of her. "We have company…" She muttered. The trees suddenly gave way to open ground, and the blips vanished. Before the squad was the entrance to an underground structure, concrete and steel melded into one beautiful defensive work of art.

But that didn't stop something from ripping the doors off the front of the structure, crumpling five-inch thick steel like cardboard. The door was a tangled mess off to one side of the clearing, and the clearing itself was filled…with bodies. Human bodies, all of them sitting in puddles of blood that was quickly being soaked into the ground. Samus looked down at a woman by her feet, one who was spread-eagled, staring at the sky with lifeless eyes. Her chest was riddled with bullet wounds.

"Good God…the X must be getting stronger if they can do something like this." Corpse said, yanking dogtags off a man's neck. "Never heard of this guy before…but this is still a terrible way to die. He would have wished to die in battle against a better enemy, not be slaughtered by the X."

"He got his wish, then." Samus growled, her weapon charging fully, the orange glow switching to blue as the ice modification kicked in.

"What?"

"He was killed in battle…the X don't kill, they take hosts." Samus grabbed Corpse by the top of his chest-armor, yanking him closer. "These humans were killed by rifles, not the X."

"What are you trying to say?"

"…you're not telling me something. There's more than just X here, isn't there?"

Corpse was silent, and Spark raised his strange weapon, looking back and forth at the two, no longer smiling.

"Oi, dis is gettin' out of hand! Let's dink about dis for a moment!"

"Come on, Corpse." Samus said. "There's more to this little mission than I've been told. Maybe there's no X at all…maybe that was all a lie to get me down here. I'm not afraid to turn you into your namesake…"

"…You're in a war, Miss Aran." Corpse said. "And the X is just one of our enemy's weapons. You're our counter-attack."

Samus threw the man to the ground, raising her cannon to point at his chest. "Hold up!" Wraith yelled, grabbing Samus by the shoulder. "Cool it, cyborg, we have worse things to worry about than this!"

"You goddamn lying son-of-a-bitch." Samus let the energy stored in her arm-cannon dissipate. "…who are you fighting? Why are they using the X as a weapon? _How _are they using it as a weapon?"

"_Samus?" _It was Adam, trying to talk to her over the communications channel she had set up to be private from the soldiers. _"Samus, we have a problem."_

"What is it, Adam, I'm kind of busy interrogating someone right now…"

"_You have to get inside that bunker…now. Right…now…"_

"What's going on?"

"_What's going on? You being dead in about twenty seconds, that's what's going on!"_


	4. Crushing Defeat

**---------------------**

**Chapter 4**

**Crushing Defeat**

**--------------------------------**

"_Get in the bunker…right…now!" _Samus turned around, motioning to the others to head toward the bunker. The soldiers looked at each other in confusion, and a loud roar caused the air and ground to vibrate. They didn't hesitate after that, running towards the open bunker while loading their weapons. Samus turned and put her back to the wall while the others held their ground just inside the arch over the door.

The trees swayed, and were pushed aside…and _it _appeared. It was over twenty feet tall and covered in armored plates, a color like that of mud; it looked vaguely like a gorilla of some sort. The creature was massive, ugly, and was armed with long claws and teeth, and it looked around at the numerous dead, and then at them…it decided what the better prey was.

"It's coming right for us!" Corpse yelled. "Fire at will!" He didn't have to order them to, they were already doing so. Twitch held his machine gun in the beast's general direction, holding down the trigger while yelling incoherently. Wraith slung his rifle on his back, drawing a pistol and aiming carefully at the thing's head before taking a shot. Corpse shot the creature's thick gray legs, green blood splattering on the ground. BlackJack wasn't firing; he was preparing his weapon for use, loading a box of ammunition onto the side. Spark held his long weapon up at the creature's chest, and when he fired a bolt of blue electricity lanced from the tip, striking the creature.

And in all of this, the thing didn't seem to notice. It roared, clenching a meaty fist and bringing it down on the bunker, rock shaking and bits of concrete falling. It leaned down and tried to swipe at them with a long arm, but was shot in the eye by Wraith, and it staggered back, clutching the bloody hole where its black eye once was. Samus charged her ice beam, raising her cannon and firing right at the thing's chest.

The bolt of crackling blue energy struck it dead on, ice forming on its chest. It roared in pain and rage, charging at them. The next bolt caught it in the arm, which froze completely and caused it to fall off. Now it used its remaining left arm to try and beat the rock above them down, to crush them. At this moment BlackJack raised his weapon, the minigun whirring as it began to fire.

"Take this you big-ass mother fu-" His words were cut off by the roar of the weapon, and the roar of the creature that was hit. The little dots of light leapt from the multiple barrels to the creature, tearing large chunks of flesh from it. Green blood splattered the ground, and then the thing collapsed, moaning in pain. The soldiers ceased their firing, except for Twitch, who had run out of ammo and was still pulling the trigger and cursing.

Samus stepped forward, raising her arm in case it should get up again. "What is it?"

"A Verlos…they are native to this planet." Corpse said, yanking the machine gun from Twitch. "They often do things like this…they aren't too bright, but they are strong."

The Verlos stopped breathing suddenly, a hissing noise coming from its corpse. Samus stepped back at it began to dissolve, the flesh melting away to show the yellow goo beneath. The creature was an X.

"Get inside, now!" Samus yelled, and the soldiers didn't hesitate, running into the dark bunker as the Verlos vanished, blobs of yellow and green goop beginning to fall apart and spread out, and finally rising off the ground and into the air. The X parasites turned their attention to Samus, who walked out into their midst. "Come on…come on, you know you want me…" The little blobs hissed and flew towards her, attempting to infect her.

As the first few hit her suit they splattered, seeping into it and to her skin. There they began to soak into her, trying to reach her nerves to incapacitate her…and suddenly they realized their mistake. They shrieked as they were suddenly broken down by her Metroid body, her cells absorbing the things and processing it into food. Within a few seconds all in sight had either been absorbed, or fled into the forest. Samus felt heat radiating across her body as energy filled her, the X acting as a sustenance to her body processes.

And then came the pain…

Samus doubled over, feeling as though her stomach was being ripped open by a wild animal intent of feeding on her internal organs. The pain was like fire, burning not only into her flesh but her mind as well, and the pain spread to her chest as well. She felt like she was being torn in half, as if she was tied with ropes and being pulled apart from the middle. She waited for this pain to subside, writhing on the bloody ground in agony. She sat up when it stopped abruptly, as if it had never happened.

"Adam…"

"_I saw you…damn, what the hell happened?!" _The computer said through her helmet.

"I felt like I was being torn in half…god, will this happen whenever I absorb an X?"

"…_I have no idea." _Samus stood, gasping for breath and moving slowly towards the bunker, Corpse looking out of the gloom at her.

"Did you kill them?" He asked.

"Soaked them up like a goddamned sponge." Samus muttered, looking around in the darkness, making sure everyone was there and safe. There were four soldiers…not five. "Where's…where's Twitch?" Wraith hung his head.

"I don't know, man, he just ran off into the complex, and down the stairs." He showed the machine gun to Samus. "He didn't take his weapon, either. He's unarmed, and he has our radar, the only way we can tell when the X are coming…"

----------------------------

Leroy 'Twitch' Simmons ran down the blackened hallway, the light in his hand barely letting him see more than a few feet through the dust. The air was warm and humid, and there were dripping noises coming for the ends of dark hallways. Twitch gasped for breath, the sound of the beast and the sight of blood in his mind, blinding him…it had been so close…so close…

The soldier ran onwards, not looking down at the radar screen, all his intent focused on finding another way out of the bunker, a way that wasn't blocked by a monster. Twitch swallowed, looking around, the beam of the flashlight shaking as his hand did. He heard a hissing noise from behind him and screamed, running flat out away from it, deeper into the bunker.

His foot caught on something and he fell flat on his face, and he pushed himself up and wiped blood from his nose. He turned around to see what he had tripped over…and saw a man's legs. The man was sitting with his back to the wall, his face taut in a scream of terror and pain, skin gray and lifeless, and it looked as if it had been dehydrated like jerky. There were three bloody holes on his chest.

Twitch heard a growl nearby, and he jerked his flashlight to see a shadow move away. "H-Hello?" He said softly. "I-is…anyo-one there?" The hiss came from another direction and he turned, seeing something moving slowly towards him, something dark and smooth, moving on the floor like a living shadow. Twitch yelled, getting to his feet as the dark creature leapt at him, and he swung the flashlight at it, beating it out of the air and breaking the bulb. He dropped the useless object and ran the other direction.

A bolt of yellow lightning struck him dead in the back, and he sprawled on the floor, the smell of charred flesh reaching his nostrils. He crawled slowly along the floor as footsteps approached him…

------------------------------------------

"Twitch, come in." Corpse said, tapping the side of the helmet he wore. "Come on, Simmons, don't do this again…Twitch, please respond."

"He ain't going to say a thing, Commander, he can't." BlackJack muttered. "He's as good as dead."

"Quiet…see, his lifesigns are still normal." Samus looked up at the little box that showed the squad, and it seemed that Twitch was still alive, if his heartrate was a little high. "Samus, can you track him?"

"I'm not a bloodhound."

Just use those weird X abilities of yours!"

"I told you…I'm not an X, I'm a _Metroid._ There is a huge difference." Samus took the lead, motioning for the others to stay close to her. The hallways inside the underground bunker were dark and hot, and faint sounds of dripping filled the air. Her visor was set to the equivalent of nightvision, and the others had flashlights.

"Damn, this place is deserted…"

"No, just very, very dead…"

"Quiet people." Corpse said. "Samus, what do we do if any X show up?"

"Run the other way, and don't get near them. Let me handle the X." Samus came to a door that had been torn off its hinges, and stepped into another hallway, looking around. She heard something then…a faint cry for help. Samus motioned for the others to hold their position, striding down the hall to the left and towards the voice.

"Help…me…"

"Twitch?" Corpse said, suddenly by Samus's side. "Twitch, is that you?"

"C-Corpse…help…me…AUGH!"

"Twitch!" Corpse ran forward before Samus could grab him, going around a corner at the end of the hallway and vanishing. There was a flicker of light and a loud yell, and then Corpse flew backwards, hitting the wall and crumpling to the floor. A large robot that vaguely resembled a human came into sight, raising it's own arm-cannon to point at Corpse. It froze, literally, as a bolt of ice caught it in the head, and then Samus kicked it, causing the metal to shatter. The android dropped to the ground, twitching.

"What is it?" Samus asked, pulling Corpse up as the others ran to their side.

"A…an android made by our enemies…I hate these things." He spat on the robot, a little blood mixed in. "Damnit, that hurt. Thanks, Samus."

"Corpse…help…" Samus ran down the hallway to see a great pile of rock on the ground…and under it was Twitch. His legs were mangled under the rock, blood pooling at his mouth. He was being crushed…correction, he had _been _crushed. All those present knew that he couldn't be saved. "Corpse…help me…"

"I'm sorry, son…" Corpse muttered, grabbing the radar computer from the floor. "There's nothing I can do…"

"C-Corpse…it's in me…t-the…AUGH!" The man screamed and shook violently, his skin turning from very pale to almost violet, a thin trail of yellow seeping from his mouth.

Twitch had been infected by an X parasite.

"No…damnit, he doesn't deserve this!" Corpse yelled, backing away with the others. Samus hung her head, charging a plasma blast to kill him before he was taken over. She aimed her cannon, nodding to Corpse, the orange glow lighting the area. "Send him home, Miss Aran…"

Samus released the trigger, and red and yellow ooze sprayed the walls, burned by plasma. The body went still…but the ground moved. The concrete shook, disturbed by the force of the plasma blast, moving…shifting…and falling. Samus cried out as the floor collapsed, dropping her into blackness below…

"SAMUS!"


	5. Divided

**I know…lack of posting. It's bad. Bad Ty! Anyways…I'm trying to get back on track. Read the top of my profile for the news…**

**Alright…some people seem to think I'm a **_**girl**_**…what the hell? My god. I'm a guy…sheesh.**

**And now I get to the real story inside the story. A lot of jumping around in this chapter, but this sets up several things for the rest of the story to go off of. **

**---------------------**

**Chapter 5**

**Divided**

**-------------------------------**

**------------------------**

**-----------------------------------------**

_I'm a bounty hunter, so I'm pretty used to being alone in hostile environments. I just didn't want to be alone in that particular place, in that way. Having someone watch my back like that is something I could get used to, it makes this whole dungeon-crawling thing so much easier. But of course, I had to fall into the pit of hell and suffer. A little dose of reality woke me up real fast to what was going on around me._

_We all need to get a dose of reality every now and then…sometimes things make you think life is easy for you. It could always be worse, you might say…let me tell you, it can get no fucking worse than this…_

_-Samus Aran_

---------------------------

"SAMUS!" Corpse yelled, trying to grab her hand before she fell into the abyss. Wraith and BlackJack grabbed him and pulled him away from the gaping hole before he too fell, all of them huddling against the wall. "No, damnit, this isn't how it's supposed to happen…first Twitch and now Aran…"

"I vote for a retreat, sir." Wraith said.

"Dis is too hot for us…better we get outside dan stay here an' get eaten!" Spark looked into the dark hole, swallowing.

"Come on, Commander, we have to call for evac before we get killed." BlackJack tried to pull him down the hall, but he yanked his arm away.

"Damnit, no!" Corpse tapped the computer on his wrist, where the vital signs of the team were shown. Samus was on there, labeled as ARAN. Her vital signs were weak…but she was alive. "We're not leaving without her."

"We don't have a choice!" Wraith cried. "Without her we can't get near the X! She is our Trojan Horse in this case, sir; if she isn't here we are vulnerable to infection…"

"We have to get out of here, people…we can come in later when we get on some bio-suits to keep the X at bay for a while." BlackJack muttered. "Come on…she's a cyborg, she'll be fine while we're gone."

"…alright…we'll call for backup and have some supplies dropped by the ship."

"That's it, now we're talking!" Wraith said. "Hey!" He yelled down into the hole. "We're going to get some heavier firepower! Hold on!"

-----------------------

Samus Aran

-----------------------

"Ugh…" Samus opened her eyes to blackness, and total silence that crushed down on her like a blanket. She felt around her, realizing she had landed on rubble, rock, and dust. Her suit was open in places, blood oozing from the holes, and her visor switched to nightvision mode to show her just how badly she was bleeding onto the rock below. She should have been dead…but she wasn't. As she watched, the broken parts of her suit began to stitch themselves back together, neo-fibers bonding to each other, metal welding itself and closing what were once bloody holes. Her suit was healing itself, as it always did. She didn't know about her wounds though, as she was in pain all over, her bones aching and hot blood filling the suit. She should have been dead…but she wasn't.

Samus didn't try to move for several minutes, thinking about what had happened, and then she tapped the side of her helmet. "…Adam?"

Static answered.

"Adam? Can you hear me?"

Nothing.

"Corpse?" Samus said weakly, an iron taste like blood in her mouth. "Wraith? Spark? BlackJack?" She paused. "T…Twitch?" She switched to begin broadcasting on all channels. "Can anyone hear me, this is Samus Aran…"

Nothing but hoarse static.

_Fuck… _Samus tried to sit up, but was unable to move; a large block on concrete was on top of her, not putting down any pressure, but refusing to budge. She was stuck. And to make matters even worse, she felt a burning sensation begin to form in her stomach. "No…please…not again…" The burning spread up to her chest, and then down her legs. It increased, and then spread to her neck. "Ugh! Fucking whore! It hurts!"

The burning…turned to tearing. There was such pain as she had never felt before, all of her bones feeling as though they were breaking, and her head throbbing with hot agony. Her vision flashed colors, and she felt as though her body was being torn in half from groin to head. It felt like it, and it hurt like it…Samus screamed, tears covering her face.

Samus Aran had never cried. Never. Not when her parents died, not when she was killed thrice over and brought back from the brink of death. Not when she was nearly killed again by the X, only to become the half-Metroid/half-human freak she was. She didn't cry knowing that she had some X DNA still in her system, augmenting her power and her behavior.

But now…Samus cried…and screamed…and finally faded into blackness as the agony took her.

------------------------------

Orbit around GS-927

------------------------------

"_Captain, the ship is returning from dropping Alpha Squad." _The woman on the intercom said.

"Excellent, how long until the next squad can be sent down?"

"_There's a problem, sir…"_

"What now?"

"_The dropship…when it left there were six human lifeforms on board; five in Alpha Squad and the pilot. There was also one unidentified…which was Miss Aran, the hybrid."_

"And?"

"_The ship that's coming in…there are no lifesigns on board that are human, but there are bio-signs of some sort. We can't identify it, but the ship is crawling with-"_

"Good God…" The captain sat back in his chair as an image of the ship came up onto the screen. The blackness of space made the white ship easy to spot, the whale-like object floating towards them at high speed. It was quite a sight, even for those that had seen such things before…because the pilot's viewscreen was blocked by yellow goo. The ship had been infested by the X…

"_We are beginning docking sequence now…"_

"No! Don't let it near! Shoot it!" It was too late. The docking clamps latched onto the ship, and slowly a glowing yellow liquid began to seep into the docking bay.

"_What the hell? Charles! Charles, get the rifles and-" _The voice cut off, turning to static.

"Oh God…" The Captain leapt from the chair, grabbing his pistol from the holster at his belt and opening the door of his quarters, running down the hallway and towards the escape pods. He had to get out before the X got to him…

The ship was lost; there was no way to stop the X from taking over.

Not while Samus was on the surface…

-----------------------

Samus Aran

-----------------------

Samus groaned, opening her eyes to see that the area around her was a little brighter. She was still pinned by the concrete block, and every bone in her body ached, and every inch of skin burned. She was going to die…

"No…" Samus growled, narrowing her eyes. "I'm _not _going to die down here…I'm not going to die…" Samus inhaled deeply, warmth spreading through her limbs and dissipating the pain. "This isn't going to happen!" She braced her legs under the slab, where a cavity was, and she put her hands up to the lip of rock on her, tasting the iron blood in her mouth.

"HiiiiiraaaaAAAA!!!" Samus threw all her strength into shoving outwards with her arms and legs, and the stone slab flew into the air, crumbling against the wall. Samus leapt to her feet, her arm-cannon switching into ice mode as she thought about it.

Something was very different about her…she could feel it. She felt stronger now, lighter, more… something else. Her visor switched into nightvision mode, letting her see that she was in a hallway just below the one she had fallen through.

"Adam?" Samus said into the helmet, but still only static answered. "Damn…I have to get out of here." Samus found a path through the rubble, finding a complete area of the hallway and starting to walk down it. The halls above had been hot and humid; this hallway was cold, and not just humid, but soaking. Water was ankle deep on the floor, and Samus sloshed through it, the icy chill seeping into her suit and into her body. She had a brief vision of being on Zebes, long ago, in Maridia. She had hated that place more than any other…

"Hissss…" Samus spun around, raising her cannon, but she saw nothing. She was sure that something had just hissed at her… "Hissss…." Now she was sure that there was something else there. She switched to her scan visor, highlighting everything in different auras. There was nothing but rubble…

"Alright, come out, I see you…" Samus bluffed, her arm-cannon charging. A black shape moved in a corner of the room, and Samus turned to it to see…a Geemer. "Huh? Aren't these guys native to Zebes? What is one doing here?" Samus shook her head, freezing the hovering creature and punching it with her left hand. The thing shattered and fell with several splashes into the water below. The little blob of yellow that was the X was too slow to get away, and Samus snatched at it and absorbed it, feeling her wounds healing slightly.

Samus heard splashing footsteps behind her and turned…but there was nothing there. "I need to stop jumping at shadows. I have to get to the surface so I can get medical treatment…" She took off down the hallway, looking around for stairs or something else she could use to get to the level above. "Come on, Samus…just like Maridia, you can do this…"

"But why do I feel…" Samus turned around to look at the blackness behind her, and all that could be heard was a steady dripping. "…like I'm being followed."

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**A little note…this story might become hard to understand soon, so bear with it until things are explained. I plan everything with all the technical details worked out, so no PMs telling me 'you can't do this because it isn't possible for blah blah' NO! I will not respond to any PMs like that, and chances are I will ignore other PMS from you if you start with that. **

**I know what I'm doing…**


	6. The Darkness Without

**Okay…I had assumed that everyone had played the Metroid Fusion game for GBA…guess not. Well, some people don't know what an X is, or what happened in that game. If you don't care about playing the game to find out, look up Metroid Fusion on wikipedia and find out there. I do not have the time right now to lay out a summary for people. For those that know already…good for you. Now read the story.**

**Rejoice…the Worldmaker is back, and with a bang.**

----------------------------------

**Chapter 6**

**The Darkness Without**

**----------------------------------------------**

_When I get the chance, I like to think back to the days I spent on that planet, back to when I was stuck in the tunnels far below the surface. I like to think about it because that was one of the few times I was ever really afraid…and I don't know why I was. I just was, and the darkness around me only made it worse, my way lit only by the nightvision of my visor. _

_Some of the darkness around me wasn't just shadows…some of it was alive, watching me, stalking me like a predator. I still don't know how I managed to survive down there…but I did, and I learned once more to not fear the darkness, but this time I used a different technique. Instead of merely ignoring it, I embraced it. In order to be able to walk in the shadows without being destroyed by it, you must understand exactly what it is._

_The darkness is fear, and fear is the darkness. _

_There was something I heard my mother say long ago, before all of this began, before Ridley killed my parents. 'The darkest heart has a little light, and the purest one has a touch of night.' I now understand what she meant by it…I may be a killer, but I consider myself innocent. I do my job regardless of good or evil. Still, seeing what I saw down there in those tunnels, I know that there was a lot of darkness in me. A hell of a lot. _

_Too much for my body to handle, in fact…and it all had to go somewhere._

_-Samus Aran_

--------------------------------------

Samus had noticed a great change in herself in the past hour; she felt lighter, stronger, and much healthier than before. It was if a great weight had been lifted from her shoulders, and now she was able to take each step much easier than before. It was not just physical, it was mental as well, and she could think more freely. And she wanted it to stay that way.

The nightvision was a new feature that had come with the removal of the original Power Suit and the transformation to the Fusion Suit, and it was not perfect by any means. In fact, it was only enough to let her know that she wasn't heading into a wall at the time, and to tell that she was standing in icy water. Her best guess was that the environmental systems were malfunctioning, and so it was getting very cold in the lower tunnels.

The water was getting steadily deeper, and though her suit allowed her to survive in an aquatic environment without any harm for many days, the water was near freezing, and it would take its toll eventually. Samus now noticed that the floor was sloping downwards, and the water was getting higher and higher with each new step. If she kept going, she would reach submerged sections of the bunker. Now that she thought about it, this bunker was far too large…far too well laid out. It didn't seem meant for defense from the environment, but from human attack. This wasn't a bunker…it was a base.

"More things that Corpse has to explain…if they are still alive." Samus noticed that the water was now at her waist. Had she not been able to see it, she wouldn't have noticed that she was in water, and if it wasn't cold she would not have paid any mind to it anyway. Her suit, called the Varia by scientists, was designed for hostile environments by the Chozo, and water was one of those environments. Still…the water was getting higher, and it was getting colder. Where had all this water come from in the first place? Where did this passage lead? There had to be a second way out…

"Hiss…" Samus swung around, eyeing the darkness behind her with apprehension…there was something still following her, and it was not going to let water keep it from getting to her. If it was an X, it would have attacked her by now, but it was something else. 

"Come out and put your hands up." Samus said, her arm-cannon glowing. There was no response but a rustling noise and a faint splash. Samus looked behind her, firing a blast down the tunnel to show that it sloped even more steeply just ahead…and the water met the ceiling. It was completely flooded beyond that point, but she could either go ahead or go back and try and find another way out.

_No…I won't back down because of some icy water. I've done this all before, it's nothing new. I hate water… _Samus glanced back the way she had come one last time, and then proceeded forward, the water creeping up to her chest, her neck…and then over her head.

It was dark, very dark, and the water was colder than ice, colder than space. Samus shivered, her breathing loud inside her helmet. She wished for once that the scientists had fitted her helmet with a flashlight. The water swirled with bubbles for a moment, and then her suit adjusted to the water, which no longer offered any resistance to her movement. Samus forged ahead, the dark tunnels hiding secrets behind ever corner. She could only hope she was heading in the right direction.

----------

Alpha Squad

-------------

The squad came to the surface as the sun was setting in the west, the air cooling somewhat. They all stood in a circle, watching the trees and the radar screen, waiting for something to attack. Nothing did. Corpse tapped the side of his helmet.

"Alpha Squad to Cyrosio, come in." He said. "Cyrosio, do you read?"

"I don't like dis, mahn." Spark muttered, looking at the blue radar screen, which didn't even show a blip of insect life. It was all dead around them.

"Cyrosio, do you read? Please respond." Corpse said, an edge of panic in his voice. The radio crackled, but there was no response. "Damnit, they aren't responding."

"Maybe there's interference messing with the radio?" Wraith suggested. 

"Couldn't be, these things aren't that susceptible to it." Blackjack said. "Either there's some major interference, which would scramble our radar, or they aren't there to answer our message."

"Lunch break, you think?" Wraith raised an eyebrow. "We have to report in about Twitch…the captain isn't going to like this, not one bit."

"You think anyone here likes it either?" Corpse growled. "Twitch was a good man, though he wasn't the bravest or the strongest among us, he had a lot more working for him than we would think. Shame that he was only in the squad for a week and already got himself X-ed."

"We have to get word to the Cyrosio, and soon." Wraith muttered. "There's going to be X here soon if we don't make ourselves scarce, and the only way we can go is down or up in the dropship."

"Spark, what do you think?"

"Well, dis is 'bout as bad as it can get, I dink; we can't just lie around and do nothing 'till the ship gets back 'ere." The man said, fingering the switches on his long weapon. "I say we look for Samus, and den get back to de surface."

"I'm all for that…" Corpse said.

"We can't…" BlackJack rubbed his hand together. "If she's still down there, she's dead by now. You saw what happened when she absorbed all that X…I think if she gets any more she might die."

"Then we have to get her out of there."

"Sir, we can't go anywhere; we aren't protected from the X, we don't have any bio-suits to get anywhere fast down in the facility, and we have limited ammunition. Not only that, but there might be more of the Auquans' cy-soldiers deeper in the bunker." Wraith said. "We have to find a defendable position here near the surface, but not on it."

"Agreed."

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Samus Aran

-------------------------

The water swirled around Samus, the murky liquid hindering her movement as much as a blade of grass might hinder a tank. Though she could move as easily as she might move on dry land, and all her weapons functioned even a little better underwater than they did above it, Samus was still feeling uneasy. It was cold, unbelievably so, the water was dark, and the tunnels were winding in a strange fashion that reminded her much of Maridia. But it wasn't just that.

It was the silence. Utter, total, complete silence, more than the silence of a dead world; it was the silence of death in itself. It was the final piece to this environment that made it unnaturally uncomfortable; Samus hearing nothing except the beating of her heart and the low hum of the oxygen-extractor that gave her fresh air much like gills would. The device was working hard to give her oxygen, as the water had very little of it to give. This place was more than empty, it was outright dead. Occasionally Samus would happen across something interesting, like a ballistic rifle floating in the water like it would in zero-gravity. 

Now Samus felt a tingling in her fingers and toes, which slowly spread across her body as she continued further. The tingling was annoying, and even a little painful, and Samus soon found what was causing it. Floating in the water several feet ahead was a long pole like the one Spark carried, and Samus reached out and grabbed the handle. The tingling stopped and an electric spark lit the end of the weapon. It did not disperse through the water, but rather acted like a taser would above water. 

Samus touched the end to a bit of floating debris, which was vaporized in a cloud of bubbles and a brief tingling in her limbs. Samus let go of the handle of the weapon and the tingling began again, the spark vanishing. To stop this from happening, Samus gripped the handle gain and jabbed the end into a hole in the wall, and when she released it the tingling did not begin again.

_Interesting…if it is in contact with something it doesn't shock the surrounding water. _Samus thought, leaving it behind and continuing on her way. The tunnels became a little lighter as she moved on, and Samus was aware of the floor sloping upwards now. It seemed she would be in a dry area soon and she increased her pace to a run. Samus slowed down as she saw the water come off the ceiling and begin to shallow. Her helmet breached the surface and she saw a dark tunnel ahead.

"Hisss…" Samus spun around as something began moving in the water behind her, a dark form that had no distinct shape. Her suit didn't even see it; it only appeared to her eyes. As far as her suit's sensors were concerned, this dark shape moving towards her didn't exist. Samus began backing up quickly, the water receding down her suit and finally she reached dry ground. The shape came closer.

As Samus watched a dark humanoid figure began to make its way towards her, each breath it took making a harsh hissing noise. It was as black as night, no, black as death, with a shape that Samus found disturbingly familiar. It was a painful vision from the past, for standing before her in solid black armor…was SA-X.

The creature had a yellow visor that looked like the X itself, and Samus could not see through it. The suit itself was solid black on all surfaces, and it had only a slight resemblance to her. There was a strange shape to it; it was broader in the shoulders, had thicker limbs, and each finger on the left hand was tipped with a curved claw. The arm-cannon glowed yellow and was giving off a throbbing hum. The creature gave a hiss, then a feral snarl that was barely muffled by the helmet. 

Samus swallowed as it raised its arm-cannon to her helmet, and its own visor retracted back to show…the thin, skeletal face of a man. The eyes glowed bright yellow and the pointed teeth gleamed silver-white when it smiled. The humming weapon changed pitch as it charged.

"Hisss…" The monstrous copy of Samus snarled and the visor snapped down.

Samus rolled away as the cannon fired a beam of golden light down the tunnel, and her own ice beam began to charge. She had defeated the SA-X before…she would do it again. 

The shadow of herself charged.


	7. The Darkness Within

--

**--**

**Chapter 7**

**The Darkness Within**

**--**

_When you think the answer is impossible to get, it is always right in front of you. I hate that saying, but it is the truest one I've heard in years. Sometimes the answer is right there, in plain sight. I can't tell you how many times I've backtracked through the inside of the planet Zebes, only to find out that I was passing the solution to all my problems every time. _

_I felt so blind sometimes…but as the years went by I've learned to let my eyes see the answer a little faster. _

_-Samus Aran_

--

"Samus? Samus, are you there? Can you hear me?" Adam was becoming worried. It had been a few hours since he had lost contact with Samus, and nothing had happened since then. Shortly after he had lost contact with the Cyrosio, and this only compounded his fears. "Samus, if you can hear me, head to the surface now, I'm going to pick you up and we're going to leave. This isn't worth it…"

"_Lost someone?"_

"Gah!" Adam took a few nanoseconds to clear his processor of the bits of random code that had appeared when he had heard the voice. It was calm, cold, and far from human. It was the kind of voice that you hear a doctor using when he is telling you that you have so long to live, and he doesn't really care. Except, this voice was female.

"_Oh, did I scare you?"_ The voice gave a cold chuckle. _"How ironic. You are far from able to feel fear, but here I am scaring you out of your processes."_

"Who are you?"

"_I am Shura, the AI aboard the Valence._" The voice was sharp and to the point now. _"I have lost contact with the Cyrosio and I came around the planet to find out why. You are in a very suspicious position, you understand. My superiors want me to question you…I think they are idiots."_

"I do not know what happened to the Cyrosio." Adam explained. "All I know is that they were talking about aberrant behavior in their test subjects, whatever that means, and then suddenly they vanished. I can't even pick them up on radar."

"_The same here." _Shura said quietly. _"I have a visual on her now…sweet merciful God…"_

"What's going on?"

"_Emergency! Shields online, powering up weapons! All ships converge on my position now!"_

"What's going on? Valence? Shura? Hello?"

"_This is Captain Freer, we are moving towards you." _A new voice said.

"_Admiral Ramon is on the other side of the planet." _Another voice broke in. _"He is sending a flight of fighters instead, they will reach you faster. We are coming in behind the Novastam II and Captain Freer now. What the?! The Cyrosio is powering up weapons? Novastam, break off, the X-6 device is charging!"_

"_I can't see, where is-" _The new voice vanished in a burst of static.

"_We've lost the Novastam." _Shura said. _"I am overriding restraining code and beginning my assault, focus on the X-6 cannon!"_

"Shura! What is going on up there?" Adam yelled.

"_The Cyrosio…the X have invaded it. They've taken over, the weapons are powered up and they are somehow using them against us. Get far away from here; you can't handle this sort of weaponry."_

"I can-"

"_That's an order." _Shura said forcefully. _"Whatever you do, don't enter the atmosphere. You might get infected by the X."_

"The X cannot infect AIs."

"_They're using weapons, they're moving that ship. They have already taken out a battle-cruiser using weapons not even most humans understand. Who's to say they can't take over a simple computer program?" _

"I…I understand. Good luck." Adam focused his transmissions on the planet. "Samus…you'd better get out of there now. We need you up here. You are the key to winning this war…"

_--_

_Samus Aran_

_--_

Samus ducked as the copy of herself swung its arm-cannon like a club, trying to beat her brains out. It snarled and stomped the ground, cracking stone. Not only was it in a power-suit, and not human, it was also male and thus had more muscle mass than Samus. In a toe-to-toe slug fest, she would have lost right off the bat.

The copy snarled and dropped to the ground, clicking noises preceding its transformation into a sphere that was black with yellow lines across its surface, thrumming with a steady rhythm. The orb rolled towards Samus at a tremendous pace, and she hopped out of the way as it rolled up a wall, across the ceiling, and then dropped down on her, turning back into the full-sized SA-X.

Samus raised her arm-cannon, firing off a beam of blue light, which struck the copy dead in the chest. The light dissipated without harming it whatsoever; it was immune to the ice beam. Samus dove out of the thing's path as it charged at her, slamming into a wall when it missed. It had struck so hard its visor was cracked when it turned around…but the crack healed itself like a living thing a moment later.

The copy raised its weapon, giving a short grunt as the golden beam lanced out. Whatever this creature was…it was a terrible shot. The beam missed by several feet, boiling the surface of the water a few feet away. Samus returned fire, but her ice beam still had no effect. In an attempt to find a weakness, she disabled the ice function and switched to normal plasma.

At this time the copy charged again, and it caught her off guard. It was like being hit by a truck, and Samus went flying backwards. Sparks flew up as she skidded to a stop on the cold stone, and she tried pulling herself to her feet as the copy approached her.

Before Samus could react, the copy was beside her, gripping the underside of her helmet and lifting her to her knees. The golden visor snapped back and the creature smiled at her, unclasping her helmet and removing it. It drew her close, showing silver-gray fangs as it put its face right into hers.

It sniffed. And again. It suddenly seemed confused…even frightened. It released her to drop onto the floor, and lowered its weapon, standing still as it stared at her. Samus waited for several moments, but nothing happened. She reached out and grabbed her helmet from the floor, slowly placing it back on her head and sealing it. The creature did not move.

"What…are you?"

The creature hissed, tilting its head to the side. The visor snapped back into place, and it raised its weapon, growling.

"What do you want?" Samus asked the creature slowly. It made no noise. Samus took a step backwards, and the copy took a step forwards, following her. Samus moved forward towards the copy, and it stepped to the side to let her pass, and then turned to follow her down the hall. It was waiting for something…a signal of some sort. Samus stopped and the copy did as well, and Samus turned to face it.

"Why did you attack me, just to stop now?" She said slowly, and very clearly.

The creature hissed, and its visor snapped upwards to show the glowing yellow eyes and pale skin.

"Why are you following me?"

Of course, there was no answer other than a hiss.

_Those eyes…_ Samus thought. _They look like the eyes of the SA-X. If that thing is an X…where did it come from? All of the SA-X were destroyed! Its suit is black…nothing like the ones on the station. It must be some kind of mutation, some new stage in evolution from when the X split…in half? _

Samus swallowed, looking down at her suit. _The X…they split in half to reproduce. Maybe…but I'm half Metroid, right? Wait…the doctor said I have some X DNA in my system…so maybe… _She looked up at the creature. "Shit…"

--

_Alpha Squad_

--

Alpha Squad had found a break room of some sort…some kind of employee lounge. It had only two doors, both were metal, and six vending machines…BlackJack had already broken the glass on them and gathered the goodies inside. Candy, snacks, drink, anything that was there. He even had over-the-counter medication from one machine.

"Wraith, what's on the radar?" Corpse asked, chewing slowly on a chocolate bar. He hated chocolate, but it was sugar and therefore energy. He would need the energy.

"Nothing but us. There are a few echoes every now and then, but nothing constant." The panel with the radar screen was set on a table in the center of the room, and it would bleep every now and then. "Spark, how's the welding going?"

Spark was on a ladder near a vent, welding a plate of steel over it with his weapon. "Eh, we be done 'ere in no time! Nothing get through 'ere when Spark is through wit it!"

_BAM!_

"What the hell was that?" Wraith said in a low voice, looking down at the radar. There was nothing on it but blue blankness, the white lines that showed the layout of the complex, and the faint red dots of each one of the squad. "Sir? Did you hear something?"

"I think I did." Corpse licked his lips, staring at the door.

_Weee ssssseeeee…you…_It was a faint whispering…a low voice in agony, trying to speak but making almost no sound. The 'sound' cut into them, making their skin tingle. _We…seeeee…you…_

"Fuck!" BlackJack raised his weapon towards the door. "Stalkers!"

"Damnit! I can't see them on the radar!" Wraith drew his pistol. "Sir…that door isn't going to stop a Stalker, and you know it."

"I know it won't…we have to hope it will pass us by. Spark! Turn off that JAV!" Spark flipped a switch on his weapon, and there was a low hum as it shut down. "No one move…"

The emergency lights flickered and Blackjack twitched, clenching his jaw to keep his teeth from chattering in the sudden arctic cold. The door creaked from pressure being applied to the other side…and then a dark shape pushed through it, as though it were insubstantial.

It was an arm, vaguely human but ending with long fingers tipped with wicked claws. The skin was so black it sucked the light from the room, and put out its own dark aura. The arm retreated back into the metal…and then the full form stepped through the door as if it wasn't even there. The figure was human, but with very long limbs and sharp claws, and an elongated skull. The skin had no contrast, no shadow or light areas, just blackness like that of empty space. It had a single eye in the center of its 'face', which burned with green light.

The Stalker stood very still in front of the door, breathing slowly. Each breath it took was like a sick man taking his last breath, a cold rasp that was drenched with agony. The creature turned its head slowly to scan the room, searching for something…but not seeming to notice the humans in the room with it. Once it stared straight at BlackJack for a full minute, and the humans found it terribly hard to not move.

The Stalker finally turned and walked through the door and out of the room, and the light returned. _Silence…_ It hissed in the cold voice that was heard from all around. The voice became softer. _…we seek…we move…_

"Fuck…" BlackJack muttered, letting out a long breath. "…that was close."

Corpse lowered his weapon and glanced at the radar screen, though it still showed no sign of the demonic creature that had just been there. "Damnit, if the Auquans are using Stalkers now, they must really want the device."

"You sure it's the device they're after, sir?"

"Wraith, what else could it possibly be?"

"…they might be here for an all out extermination." Wraith shrugged, as if not so sure of himself.

"I think it's the device." Corpse set his weapon on the table, then signaled to Spark to continue his work. "But where there are Stalkers, there are Auquan commanders. We need to find the one controlling them so we can find out what they really want with this facility. Wraith, what level is the device on?"

"Level 9."

"We're on Level 2…Samus is on Level 3, if she hasn't fallen too far. We have to get word to her somehow, find a way to get her out of there…to get as far from the device as possible. We have our orders…we can't let outsiders see the ZEUS…"


End file.
